Shinji ZERO
by Ghost of Meat
Summary: Rei has survived Unit 00’s destruction during the 16th angel. After it is rebuilt Shinji gets called in by Nerv to be its first test pilot. When a tragedy befalls him can Nerv’s top scientists save him? pairing Shinji Asuka.
1. Chapter 1 Rei

Disclaimer- don't own it

A/N This is an idea I was working on while I was writing my other fics. Unfortunately those two got away from me and I had to stop and review them. So to fill the gap, and sate my boredom, i've been penning up some of my other ideas.  
MORE THAN LIKELY I'll actually be able to finish this one

**Shinji ZERO**

Chapter 1

"Rei, eject"

Commander Ikari's words rang in her ears. The 16th angel had penetrated Unit 00 and had begun 1st level contact, an attempt at full take over. Seeing it as her only option she used her AT Field to contain the angel while she activated the Eva's D-Drive, the self-destruct device.

"I can not, if I leave Unit 00 then the AT Field will cease to be, I will not let it"

As she pressed the lever in she was, rather violently, forced to the bottom of the Entry Plug.

From his seat aboard Unit 01 Shinji looked on horrified as Unit 00 doubled over, its core seconds from an explosive overload. Horrified, that was, until he saw the Entry Plug shoot from Unit 00's back, followed a half second later by a massive explosion which rivaled every N2 bomb her had ever seen. He spent the next minuet figuring out the plugs escape trajectory. Once he had is probable location he turned Unit 01 toward it. There lying in a thicket of trees on a mountain side sat Unit 00's Entry Plug. He knelt the Eva down beside of it and ejected his plug. A few moments later, after a dizzying ride down on the descent cable, he was at Unit 00's Plug. As he had after the 5th angel he pulled the plug hatch open with his hands. When the door finally opened he leaned in. To his shock there was no one in the plug's seat.

"Ikari"

He followed the voice to its owner. There at the front of the plug lay a very dazed, but very much alive, Rei Ayanami. Shinji climbed into the plug and retrieved the first aid kit from behind the chair. He then slid back to the front of the plug to tend Rei.

"Are you hurt Ayanami?"

She answered in her usual monotone voice, though he could tell she was in a bit of pain

"Nothing that will not heal in time, however I seem to have dislocated my right shoulder during the ejection"

"Are you sure Ayanami?"

She winced a bit as she sat up

"I…have dislocated it before; it is nothing serious the recovery team will reset it"

Shinji noticed a small cut across her left cheek

"Well at least let me take care of that cut"

He sat the first aid kit down and opened it. He removed an anti-biotic patch from the kit and opened it. He checked the cut before he applied it. It was a bit smaller than the patch so it completely covered it

"Well I don't think you'll need stitches, this should be enough"

He carefully applied the patch. Rei noticed how soft and warm his hand was as he applied the medicated patch.

"You do this often Ikari"

"Yes"

"Why"

"Asuka"

"Pilot Soryu physically harms you"

He paused for a moment, his expression became slightly down

"We use to fight a lot before…but it's gotten even worse now…after the 16th"

This infuriated Rei, though outwardly she showed no signs of it.

"She should be disciplined for this"

Shinji sighed

"No, that would only make things worse; it would give her an excuse to be mad"

Long ago Shinji had become an expert as reading Rei. Though she gave off the air of a person who didn't know of emotion, though in some cases she didn't she knew enough of them to know how not to show them. Shinji had learned to read her subtle actions and movements as well as the occasional eye twitch to determine her mood, and right now she was mad.

"Still Ikari, the major should be told of this"

"No, she has enough to worry about"

Outside the pair could hear the recovery team approaching

"Well I better get back to Unit 01; I'll come to the hospital once I get out of the showers ok"

A millimeter thin smile graced her lips

"I shall wait for you there; I am not sufficiently injured to warrant an overnight stay"

"I don't want to inconvenience you Ayanami"

"It will not be"

True to his word Shinji meet Rei at the hospital once he finished his de-briefing and had his shower. She was sitting in the waiting room still wearing her plug suit, her right arm was in a sling and the medicated bandage that he had applied to her cheek had been replaced by a thin strip of Liquid Stitch, a medicated bonding agent that had replaced conventional stitches for minor cuts a few years back.

Rei was silent as Shinji sat next to her.

"Umm…how are you feeling Ayanami"

"I am well Ikari"

He nodded, after a moment of thought he spoke again

"Umm Ayanami"

"Yes Ikari"

"We're friends aren't we?"

"I believe so, though I have never had a friend before"

"Umm well…could you…if it's not to much trouble"

"What is it Ikari"

"Could you please…call me Shinji?"

"Very well…Shinji"

"Thank you Ayanami"

"Rei"

"Huh"

"I would like you to call me Rei"

"Sure…Rei"

He paused and thought for a moment

"Umm…Rei"

"Yes"

"Would you like me to walk you home?"

"That would be…acceptable"

The walk from the Nerv hospital to Rei's apartment was a rather quiet one. Not a tense quiet but a comfortable one. Neither said a word until they reached her apartment door.

As she reached for the door Shinji finally spoke up

"Umm Rei"

"Yes Shinji"

"Umm…well…you've changed"

She tilted her head to the side

"How so"

"Well umm…you're opening up…somewhat"

She thought for a moment

"Perhaps…well good evening Shinji"

She stepped inside, as she was about to close the door Shinji spoke up

"Umm…Rei"

"Yes Shinji"

"Would you mind if I…came to visit tomorrow"

"That would be acceptable, you my come at what ever time you wish"

"Thank you, Rei"

"You are welcome, good night Shinji"

She closed the door, Shinji turned and headed for home with a slight smile on his face

"Well, it's a start"

Misato sat in her room staring at the phone, waiting for a call she was sure wouldn't come. She sat back and thought of the events of the day.

Rei had managed to eject from a self detonating unit 00 and walk away with only a dislocated shoulder and a few cuts.

She had just had Asuka placed into "protective custody" at Nerv following a suicide attempt, thank god Maya found her in the bathroom. A few more minuets and she would have bled out.

Shinji was surprisingly starting to come out of his self-loathing and level out, he was also becoming increasingly close to Rei. She could only smile at that thought.

Then there was Kaji, she hadn't herd from him in a few days. While that in its self wasn't cause for concern, this time, for some reason she was. And that's what worried her; she had never been overly worried when he would disappear like this.

Than the phone rang

"Hello"

"Katsuragi"

"Oh Kaji thank god, where are you"

"I can't say, I just wanted to let you know I'm still alive"

"Well, when are you coming back?"

"I may not be, listen I just wanted to tell you that…I love you, could you do a favor for me"

"What"

"I've been growing, melons, Shinji knows where they are. I'd appreciate it if you could water them for me"

"Only if you'll promise to come back after this is over"

"I'll try, goodbye Misato"

A few weeks had passed. Misato still hadn't heard from Kaji. The kids hadn't gone to school, seeing as how it was damaged. Rei moved in with Misato and Shinji after her apartment complex collapsed due to structural damage. The kids had gone in for weekly sync tests as usual though this week had been special. The 5th child, Kaoru Nagisa, had arrived and had under gone his first Synchronization test, his scores were exceptional.

Shinji was walking from the test plugs to the locker rooms and shower when he heard a voice behind him

"Hello Shinji"

"Huh, oh…hello Kaoru"

"So are you done for the day?"

"Yes…I was about to shower and head home…would you…like to come over for dinner"

"I would love to, thank you"

"Umm…do you…prefer anything?"

"I shall eat what is placed before me"

"Ok…I hope you don't mind Ayanami, she lives with me and Misato"

"I have not had the opportunity to meet the first child, it will be interesting"

While Shinji showered Kaoru waited outside of the showers. He noticed the 1st child walking down the hall toward the showers

"Hello Ms Ayanami"

"Identify yourself"

"I did not mean to frighten you; I am Kaoru Nagisa the 5th child"

"Why are you here?"

"I am waiting for Shinji, I hope you do not mind but I will be having dinner at your residence tonight"

"Did Shinji or the Major invite you?"

"Yes he did"

"Then I shall trust his judgment"

"I hope we can get along Ms Ayanami"

"We shall see"

After about 20 minuets or so Shinji exited the showers to find Kaoru sitting patiently on the benches, he walked over to him.

"I'm done Kaoru"

"Then shall we go"

"Umm yeah sure"

"I met the 1st child while you were bathing"

"Rei…did you tell her you were coming over"

"Yes, she just wanted to make sure I was invited"

"Oh, umm ok"

Shinji and Kaoru left Nerv HQ. They walked for about 20 min through the remains of Tokyo 3, a section of which had mostly been flattened by Unit 00's detonation. The city itself was not in horrible shape. Just that most of the people had fled after the last battle. Looking at the city now Shinji knew they would return once the final angel had been defeated.

The pair arrived at the Major's apartment. Shinji opened the door; they found Rei at the kitchen table reading and Misato watching TV, well the stations that were still on the air that is. After a moment she noticed the pair

"Huh oh Shinji, did you bring home a guest"

"Umm yeah… Kaoru I'm sure you know Misato"

"Yes I am aquatinted with the major"

Misato nodded

"Yes we've meet Shinji, so will you bee joining us for dinner"

"Yes Shinji has invited me to attend"

"Well, I'm sure tonight will be fun"

Rei, who had just joined her roommates in the living room, nodded and commented

"Yes im sure this will be both an informative and interesting engagement"

A/N well the big event of the story won't take place until next chapter. I just wanted to get the things with Rei surviving and Kaoru's appearance out of the way.


	2. Chapter 2 Death and Rebirth By Unit 00

Disclaimer- don't own it

A/N Rei will be a bit OOC in this story, but that's because I'm still using Rei 2 and not Rei 3. Sorry the last chapter was kinda rushed; all I needed to do was establish Rei and Kaoru's presence.

**Shinji ZERO**

Chapter 2

Death and Rebirth by Unit Zero

A few weeks had passed since Unit 00's self destruct. Dr Ritsuko Akagi and Sub-commander Fuyutsuki looked out into the cages where a second Unit 00 was nearing completion. Normally it takes a month or two to build an Eva even with the parts on hand as in this case. However enough of Unit 00's remains had survived the explosion to expedite the re-construction. The Eva, which for the moment only had its A-Type equipment (no shoulder plates), was sporting its blue coloration despite Dr Akagi wanting to return it to its original yellow.

"So how long until its ready" the sub commander asked the bottle blond

"Its core just arrived, its S2 organ was installed yesterday, so we should have it in and ready by test time tomorrow"

"Good" 'now lets hope Ikari doesn't pull anything' he thought

Gendo Ikari, AKA supreme bastard of the universe, sat in his office going over the final stages of the new Unit 00's initial activation test. By tomorrow morning the unit would be ready for the first test pilot. Rei would no doubt volunteer but he still needed her to accomplish his goals. The 2nd was to unstable to even sync much less control it in the fashion he needed. The 5th was also unsuitable; his score was too high to sacrifice him. That left the 3rd child; he was a thorn in his side already. Unit 01 was far too valuable to the committee to risk it's lose to the 17th angel when it arrived. Rei or the 5th child in Unit 02 would be more than enough. Or, he smirked, the 5th in Unit 02 and Rei in Unit 00. Rei was stable; she would follow his orders, even after she discovered what he had done. Or so he thought anyway.

"Yui I will be by your side soon"

Shinji sat in Unit 00's Entry plug. To say he was nervous was an understatement. The last time he was in this Eva it tried to kill him and he ended up back in the hospital. But this time it was different, the Eva was a clean slate, no one else had even set foot in its Plug.

He sat back and though of the previous night

Rei staying in his room

Sleeping on the other side of his bed

And Rei's confession

She had told him of her past, her 'creation' by Nerv. At the time he was scared, but that faded with the realization that she was as frightened as he was. Her emotionless mask was off; she didn't care at that moment.

"Rei…you mean you"

"Yes, I was created by Nerv from the DNA of the 2nd angel and Yui Ikari"

She was crying, though she wasn't crying as a normal person would, she was silent and her voice was still monotone and even, but Shinji could see tears running down her cheeks and onto her side of the pillow. Shinji closed his eyes and thought for a moment. He want sure he could handle this and kept repeating his old motto 'I mustn't run away' to himself. He opened his eyes, she was still crying. He needed to know one thing

"Rei…are you trying to tell me…that…you're my…sister"

She nodded

"Please do not abandon me"

Shinji then did something that shocked even him; he wrapped his arms around her and pulled her closer to him

"I would never abandon you…baby sister"

Hearing those words were all Rei could ever have wanted. Shinji, no her brother, had accepted her. He wouldn't leave her. He would stand by her side when ever she would need it. And even in the times she didn't think she did, he would be there. And what's more, that's what he believed.

Yes his life was now more interesting with a half angel sibling.

"Shinji were ready to begin"

"Roger"

In the control room Misato, Ritsuko, Commander Ikari, the Sub-Commander, Kaoru, and Rei stood watching the first activation test for the new Unit 00. Maya and the other Techs monitored the Eva as the startup procedure began

"Connecting main contacts"

"Now beginning insertion"

Unit 00's entry plug was inserted into the plug socket

"Monitoring sycnro graph"

0.8

0.6

0.5

0.3

0.1

"Border line cleared, now beginning pilot synchronization"

"30, 44, now at 50 percent, 60, 76, 78, 80, now stabilizing at 83 percent"

Misato looked on, beaming with pride "Shinji's amazing isn't he"

Kaoru nodded "yes I agree, his skill is impressive" 'then why am I feeling uneasy' he thought

Suddenly Unit 00 began to strain against the restraints in the test chamber; Maya noticed his sync ratio skyrocket as the emergency alarms began to blare.

"Ma'am his sync ratio is at 95 and rising"

"Cut the connection, eject the plug" Ritsuko commanded

"The connections won't terminate and the plug eject signal has been received but ignored"

"What's his Sync ratio at" Misato asked in a panic

"276 and rising, that's imposable it should have gone berserker by now"

Ritsuko couldn't believe this, this Eva was a new one it shouldn't... her thought caught her. A new Eva, a new core, and untried core 'damn you Ikari your going to use Shinji for the core component aren't you, well im not going to let you' she was broken from her thought track by Maya

"Ma'am Unit 00's S2 has become active"

"Shut it down"

"All signals are being rejected, Sync ratio now at 345 if it goes any higher"

Misato looked on, she knew what would happen if it breeched 400

"It's the same"

"The same as what" Kaoru asked

"During the 14th angels attack Shinji's sync ratio jumped passed 400 and he was absorbed into the Eva, its happening again"

At that moment Unit 00 ripped free of its restraints. It stumbled forward and fell to its knees clutching its head. With teary eyes Maya called out the sync ratio

"The Sync Ratio has leveled at 407, we've lose vitals on the pilot"

Ritsuko shook her head, she looked at her monitor and confirmed

"His Ego Border is gone, were to late"

Rei couldn't believe this, just the night before she had found her brother, only to lose him less than a full day later. Suddenly the alarms began to blare again. Maya reported

"Ma'am the plug ejection signal is now being accepted"

Ritsuko became frantic

"No abort ejection"

Too late, the entry plug rocketed from its socket in the Evas back. It hit the ceiling with enough force to crush the Entry Plug. The group looked on in horror as the LCL and remains of the plug fell to the floor below, everyone that is except Commander Ikari who wore a slight smirk, which Rei seemed to notice. Underneath her emotionless façade Rei's anger was at its boiling point. Yes she could take the way he treated his son, yes she had come to understand why Shinji didn't trust his father, and yes she herself had begun to question him. But this was too much, this was her brother, this was where she drew the line

"Major Katsuragi may I have a word with you"

"Rei now isn't…"

Rei grabbed her wrist and dragged her off to the corner of the room

"Alright Rei alright, what do you need"

"My I see your weapon please"

Misato was a bit talked back by this

"Why"

"I can not say as yet"

"Umm… I don't really think it's a good idea Rei"

"It is necessary Major"

"Ok, just don't do anything stupid"

Misato pulled her 45 from her holster and handed it, handle first to Rei. The quiet girl nodded her thanks befor rejoining the group. No one noticed her even pull Misato to the side, save for Kaoru who could tell what the quiet girl had planed. She walked up behind commander Ikari. In that brief moment a horrified Misato saw what Rei was planning to do.

Shinji definately wasn't having a good day. At first the activation test was going just fine, and then he got this mind numbing headache and blacked out for what seemed like a few seconds. As he started to come to it felt as though he had somehow found his way out of the Eva and on to the catwalk, maybe. He was on his knees that he knew, his eyes were still closed and his head was still pounding. He called out to Misato and the others, but got no answer.

'Communications must be down' he thought.

Then he decided to open his eyes, and immediately wished he hadn't. For a moment he was blinded by bright white light. He waited for a moment for his eyes to adjust before he opened them again. Again he wised he hadn't, for the body he was staring down at wasn't his own, But Unit 00's. He blinked a few times, hoping it was just his eyes playing tricks on him and that he was in the entry plug still. Then he noticed the shattered Entry Plug and puddle of LCL surrounding it. Then it his him, He had been absorbed again, by Unit 00 this time. He collapsed forward, his head coming to rest on the floor of the test chamber. He pulled his arms, well they were his now anyway, to his chest and simply sat there in shock. Then he heard some kind of commotion in the room above him.

Everyone in the control room had their eyes glued to Unit 00. That was until they all heard the cocking of a pistol. Commander Ikari heard it to, then he felt s slight pressure in the middle of his back, he knew it was said pistol though is user was a surprise, it was Rei.

"Why did you do it commander?"

He knew at this point he was in trouble, if he made any aggressive move Rei would fire. He knew her well enough to know she wouldn't do something like this and not go through with it.

"Why what Rei"

"Why did you Order pilot Ikari to test Unit 00 knowing it was untried"

"Because his usefulness was over"

"I believe you were mistaken"

Before anyone could react the retaining wall separating the test chamber from the other Cages collapsed. The commander used this distraction to quickly knock the gun from Rei's hand and grab her by the throat

"You dare to point a gun at me Rei, I made you"

She was struggling for breath

"You dare interfere with the scenario"

Rei's vision began to darken

"You will be replaced, goodbye Rei"

Befor he could finish the job the wall separating the control room from the test chamber was ripped away. To his horror, there stood Unit 01 its mouth open slightly. He droped Rei and stepped back. The Eva reached into the control room and plucked him out. He sat in the Eva hand looking up at it

"Yui"

In that moment Kaoru sensed exactly what he had come here for, Adam, he was close. Then he noticed him, he was inside of the commander some how. He also knew Adam, along with his mission, was doomed

Unit 01 closed its hand, the sound of crushing bone and squashed flesh could be heard. Unit 01 droped the remains of Commander Ikari, Which now resembled smashed hamburger, to the floor of the test cage and smashed them under its foot for good measure. Kaoru just shook his head, his mission was over, and Adam was dead, as was Commander Ikari for that matter.

Shinji was frightened beyond all description. When the wall collapsed he had scooted back a bit so he wouldn't be hit by any debris. Now he had scooted all the way back against the wall. Eva Unit 01 had just smashed through the retaining wall, ripped its way into the control room, extracted his father who at that moment was strangling Rei, and crushed him into ground meat. So of course he was afraid.

Misato and Ritsuko were at Rei's side. Ritsuko confirmed that she hadn't suffered any damage but instructed one of the technicians to take her to the Infirmary anyway just to be safe. Kaoru walked over to the now destroyed window and looked into the test chamber.

Eva Unit 01 approached Unit 00 which had scooted back against the wall opposite the now smashed retaining wall. Shinji closed his eyes and waited what he thought would be a painful end at the hands of the berserk Eva. Instead he felt a hand softly touch his cheek, well what you could call a cheek on Unit 00, which was followed by a soft soothing voice

"Do not worry Shinji; he'll never hurt you or Rei ever again"

The voice was one he knew well; it pained his very soul to hear it. He had only heard it a few times after all

"M…Mother"

Shinji opened his eyes; Unit 01 was kneeling in front of him with its hand still in place. The hard and cold expression of its eyes had softened

"Come on Shinji lets get you stood up ok"

"Yes mother"

Unit 01 helped Unit 00 to his feet; she then guided him over to the remains of the restraints

"Let's get you put back into the restraints so Naoko Akagi's girl can take car of you"

"Ok"

Unit 01 Helped Unit 00 dock back onto the surviving restraints

"Now you go on to sleep ok Shinji, they'll take good care of you"

Shinji could feel his eyes getting heavy and drifted off to sleep, still held in place by the restraints. Unit 01 turned and headed back to its cage. In the control room Dr Akagi was baffled by all of this. Apparently the souls with in the Evas DO have conscious control to an extent.

"ma'am Unit 00 has powered down most of its systems but the backups and the S2 are still online and were getting a backflow signal that, well, looks like a REM signal" Maya Reported

"An REM signal, what does that mean" Misato asked

"Well…" Ritsuko walked up to the now missing window "…it means the Eva is dreaming, if it is an REM signal"

"So, Shinji is in control of it"

"Not exactly, more like the Eva's body is now his own"

"Just what the hell are you saying Ritsuko"

At this point the Sub-Commander piped in

"Doctor, I suggest you show her, and take Rei and Kaoru to"

"Yes sir, com with me you two"

The pair followed Dr Akagi to the infirmary. Once they had found Rei the party of 4 descended into Terminal Dogma and Nerv's biggest secret.

A/N Well that's chapter 2. Killing Gendo like that was fun, even if it was a bit much.  
The next chapter will be a bit calmer though and expect the return of Asuka.  
Thanks to my readers and reviewers. And sorry if I rambled a bit im trying to be more descriptive.


	3. Chapter 3 Shinji and Rei

Disclaimer- don't own it

A/N Thanks to all of my Readers and Reviewers. You guy's and gals rock

**Shinji ZERO**

Chapter 3

Shinji and Rei

Misato, Rei, and Kaoru followed Ritsuko into the bowls of Terminal Dogma. Their destination was a small lab which bore an odd resemblance to Rei's old apartment

"So what is it im suppose to find out Ritsuko"

"Would you like to tell her Rei, or do you want me to"

"I will tell her Doctor, Major until now you have not been allowed access to any files pertaining to me, which will now change. I was created years ago from the DNA from the 2nd angel and a human donor named Yui Ikari"

"What"

Misato couldn't believe what she was being told, Rei was a lab experiment

"Yes I know this must be hard but understand, I did not chose this, Commander Ikari ordered my creation"

Misato's expression was a cross or pure horror and total anger

"Does Shinji know any of this?"

"Yes I informed my brother last night"

"Brother"

"Yes, I carry approximately 50 percent of Yui Ikari's DNA. There for I am Shinji's half sister"

"The reasoning behind this was simple Misato" Ritsuko added

"We needed a core component for the dummy plug system"

She pointed to a set of double doors against the far wall

"In there are the last of the plug cores and your answers Misato"

Misato Rei and Kaoru followed Ritsuko into the large circular room, the Clone Room

'Ah the daughters of Lilith' Kaoru thought to him self

About an hour ago Unit 00 had been moved to the main holding area with Units 01 and 02. As Shinji slowly regained consciousness he at first thought it had all been a horrible nightmare. 'Thought to soon' the thought, realizing he was still in the restraints. However the feeling of a lukewarm liquid up to the level of his knees caused him to open his eyes.

In the main control room Maya was telling her fellow Bridge Bunnies Hyuuga and Shigeru about the day's events when Shigeru noticed that Unit 00 had powered back up

"Sir, power levels are rising in Unit 00"

Fuyutsuki, now the commander of Nerv, inquired

"Is it attempting to leave the cage?"

"No sir it's just standing there"

"good, 'im going down there, Major Katsuragi and Dr Akagi should return momentarily, tell them to meet me in Unit 00's cage"

"Um…yes sir"

Misato couldn't believe what she was being told. Nerv's every secret had been placed at her feet. Rei's origins, Instrumentality, Kaoru's revelation that HE was the 17th angel It was all to much

"So let me see if I understand this Nagisa, you're the 17th but because Adam was in Commander Ikari's hand he died with him so you're harmless now"

"It is as you describe it"

"I…I need to let this all settle in, after what happened to Shinji, and now all this"

Ritsuko nodded

"I know how you feel Misato, go home and get some rest, at least 5 hours. I'll call you if I need anything or anything happens"

"Alright, I just need to sort all of this out"

Misato quietly headed out of terminal dogma and headed for home, Ritsuko looked at Kaoru and Rei

"Rei you should go to, you need to rest as well"

"No thank you doctor, I will stay with my brother, is there any way you could arrange a synchronization test for me"

She thought for a moment

"Yes I think so, it shouldn't be so difficult. Why do you want to try Rei?"

"I wish to speak to my brother; this would be the most expedient way to do so"

Kaoru nodded

"Yes that is so, however I believe the second child may also benefit from such an undertaking"

Ritsuko tilted he head to the side

"How so"

"The light of Shinji's soul still glows brightly inside Unit 00, it along with his obvious affection for her could serve to aid her recovery form Arael's light"

The older woman nodded

"Yes that shouldn't be a problem, so what will you do now Kaoru or should I say Tabris"

"I will live as a lilum, with Adam destroyed our life source is ended. We angels of Adam will no longer live eternally; therefore when my day comes I shall pass along, as all lilum will in their time"

"Though you still have your abilities"

"Yes, they are a part of me that I can not be rid of"

Ritsuko nodded in acceptance of his answer

"Alright, we should head back to the bridge and prepare for the sync tests with Unit 00"

The three left for the bridge. Unexpectedly leaving Rei's sisters, who thanks to Tabris's presents now had souls of their own, a lot to think about.

Shinji stood in the cages, his new body, or Eva Unit 00. He looked out into the cages at the other Eva's. His mother in Eva 01 was still asleep, though he had talked to her a few times since the accident. Unit 02 however hadn't said a word to him, so he decided to make first contact.

"Umm…excuse me"

"Yes" she answered in a monotone voice which reminded Shinji of Rei.

"Umm…what's your name?"

"Why do you care?"

Shinji could tell she was depressed, he remembered what had happened to Asuka at the hands of the 15th angel. This person must have gone through something similar.

"I umm…just wanted to talk to you, my mom's asleep and I'm kinda…getting lonely"

She sighed

"Yeah I know the feeling, Yui and I talk sometimes but I never really get talk to anyone new"

"Well…I'm here now"

She brightened up a bit

"How did you get in there anyway?"

"My father, he tricked me and got me to test this damn thing"

"I know the feeling, my husband; well ex-husband did the same thing. I didn't even get to say good bye to my daughter"

"What's your name?"

"Kyoko Zeppelin Soryu"

"Soryu?"

The pair spoke long into the night about their lives and by the time he fell asleep again Shinji knew he had found someone who truly could understand him

The next day Ritsuko, Misato, Kaoru and Maya sat in the control room of the cages watching as the Technical staff prepared for Rei's sync test with Unit 00. She had originally had her reservations about the tests but all indications showed that Unit 00 was more than ready to sync with Rei. Her plug was lowered into place and locked into the Eva

"Ok Rei were now beginning synchronization"

"Yes doctor"

"Maya lock in connections 1 through 236"

Maya looked at her monitor as the connections locked into place

"Connections locked ready for final connections"

"Do it"

"All connections locked, Rei's sync now at 67.5"

Ritsuko nodded

"Rei how is it"

She sat back and smiled, something no one in the room had ever seen

"Very comfortable doctor"

She closed her eyes and concentrated her thoughts

_Are you there brother?_

_R-Rei?_

_Yes brother I am here_

_Oh thank god, it's good to hear your voice_

_As it is to hear yours_

_Yeah_

_How are you_

_I'm fine actually; I've been talking to either mom or Kyoko so I'm not really lonely._

_Dr Akagi and Major Katsuragi have been at HQ nearly every moment since your accident_

_I can hear them when they come into the cage; I just wish I could talk to them_

_They are working on a system using the communications system_

_Ok, umm rei_

_Yes brother_

_Would you mind if I try something_

_What is that brother?_

_I…want to see if your can talk to mother_

Rei couldn't help but smile a bit

_Of cause brother, I am curious, does she see me as her daughter_

_Yes, im going to try now ok_

_Yes brother_

For a moment everything was quiet then rei heard a voice she didn't recognize

_Are you their Rei?_

She smiled again

_Yes…mother_

_It's good to hear your voice finally_

_As it is to hear yours mother_

_Its sweet you're already calling me mother_

_I carry your genes, you are my mother therefore it is only reasonable for me to call you such_

_Thank you, when this is all over, if Naoko's girl can free us, mabe the three of us could try to be an actual family_

_I would like that_

_Ok, i'm going to go for the time being, goodbye my daughter_

_Goodbye for now mother_

Rei relaxed until she heard Shinji again

_I'm back little sister_

_That is the first time you have ever call me that_

_Oh umm…sorry_

_Do not apologize, I enjoy it_

_You're welcome_

_Shinji, Dr Akagi will soon attempt to see if Pilot Soryu can sync. Nagisa has informed her that you may be able to help her_

_I'll try but, how does he know_

_Kaoru Nagisa is the 17th angel_

_HE"S THE WHAT_

Rei cringed

_Do not shout brother, it hurts_

_I'm sorry rei, but Kaoru is the 17th angel_

_Yes, but he is harmless at this point_

_But how_

_I shall explain, In order to keep him under control the commander had the 1st angel placed into his body, when unit 01 destroyed him Tabris's goal was destroyed as well_

_Tabris_

_Pilot Nagisa that is his name_

Shinji reflected on that for a moment

_Tabris_

_Yes, now I must go so that the attempt with pilot Soryu may attempt to sync_

_Ok, bye sister_

_Be well brother_

Rei opened her eyes, she was still smiling. Though it felt like longer the whole conversation took only a few moments

"Dr Akagi Shinji is ready for pilot Soryu"

Ritsuko tilted her head to the side

"You've been talking to him"

"Yes"

Misato butted in, worry resounded in her voice

"How is he Rei, is he ok"

"He is well; he has been spending time with our mother"

"Your mother"

"Yes, Yui Ikari"

As Ritsuko and her staff prepped Asuka for entry a group of girls walked through Terminal dogma toward the location known as Heavens Doors. Each of the 7 girls bore an extreme resemblance to Rei, though differences were starting to show. Differences like changing hair color, eye color, body shape and facial structure. With in a matter of days each would look unique.

They all walked up to the doors which slid open as their approach. Inside stood their objective, the crucified 2nd angel Lilith. The group of girls stopped at the edge of the LCL pool at the angel's feet

"Why are you here my daughters?"

The gentle voice of Lilith called; the girl at the front of the group stepped forward and spoke up

"Mother we require your aid"

"In what matter my child"

The brother of our sister Rei requires aid, he has become entrapped inside of the human construct called Evangelion, Unit 00"

"Tell me of this matter and we shall aid him"

The girl told Lilith of how Shinji came to be trapped inside of Unit 00. How his father had betrayed him to the machine and how Unit 01 had finished him. They also told her of Adam's fate and Tabris's new allegiance to his friend at which she seemed slightly pleased

"So Adam has been destroyed and his angel Tabris has placed his allegiance to my children, this is good"

From the LCL in front of the girls strode a young woman with long white flowing hair, brilliant red eyes, and pail but soft skin. She had a well developed body over which hung a simple white robe tied with a sash at the waist. It was Lilith in her human form. Each of the 7 girls hugged their mother. After which Lilith laid out her plan

"Now my children, we shall help your sister save her brother and the others trapped inside of Evangelion"

One of the girls asked

"How mother"

"Come closer my children and I shall tell you"

A/N Well that's chapter 3. What are the clones and Lilith planning you ask you'll have to read and find out in chapter 4.  
Next chapter- Asuka's sync test with Unit 00  
Will it help her come to terms with everything that has happened to her, or will it do more harm than good.

till then  
later


	4. Chapter 4 Kyoko and Shinji

Disclaimer- don't own it

A/N Thanks to all of my Readers and Reviewers.

A/N post Edit - I understand the inital reaction th this stories original pairing of Shinji/Kyoko. after reviewing it i realized the that it was a BAD idea, so i fixed it.

**Shinji ZERO**

Chapter 4

Kyoko and Shinji

Ritsuko's staff were busy prepping Asuka for her plug entry attempt. The poor girl was still nearly catatonic so Maya and a nurse at the hospital had to physically dress her in her plug suit. Meanwhile Ritsuko had completed the modifications to the com system for unit 00 which would allow Shinji to talk to them and vice versa. Misato and Rei were to be the first to make the attempt while Kaoru, Commander Fuyutsuki, and the rest of her staff who were not working on the upcoming Asuka Entry test watched.

"It's ready, channel opened"

Ritsuko said as she opened the Com line. Misato calmly spoke

"Shinji, can you hear me"

There were a few moments of silence, and then all heard what they so desperately wanted. The rather excited/relived voice of Shinji Ikari, the MAGI had synthesized is voice from the records perfectly

"Misato is that you, oh god I almost didn't recognize you, is everyone ok"

"Calm down Shinji, its good to hear your ok"

Misato, try as she might, couldn't stop tears from forming in the corner of her eyes. She was happy to even hear his voice again; around the control room many of the technicians joined her sentiments. Even Ritsuko shed a few tears

"Misato…is Rei there"

"Yes she's here"

"Hello…sister"

"Hello brother, you are well I take it"

"Yes I'm fine"

"How is mother?"

"She's fine, how's Asuka"

Ritsuko chimed in

"They will be bringing her from the hospital in about 30 minuets we just wanted to make sure this modified com line was working"

"Ok, I'm ready when ever she gets here and Misato"

"Yes Shinji"

"Umm…just in case Dr Akagi cant get me out of here, thank you…for every thing"

"Don't say that Shinji, your coming home if I have anything to say about it"

"Well, either way, thanks, umm…I guess I'll talk to you later"

"Bye kid"

"Bye Misato, bye sister"

"Good bye for now brother"

The com line when dark, Ritsuko cut the connection and turned to the major and Rei

"Well I'd say that was successful"

Misato nodded and the said

"Please tell me you can get him back"

She just sighed

"Were not to sure at this point, it's not looking to hopeful"

Rei finally spoke up and asked

"Can we do anything?"

"Not a this point no, all we can do is wait and pray for a miracle"

If only she knew

Shinji sighed at the connection cut, he immediately began to miss everyone, he needed to talk to someone, but his mother was asleep

"Kyoko are you there"

He got an instant response

"Yeah, what's up?"

"I just talked to Misato"

"Is everyone ok?"

She asked a bit concerned with his depressed tone

"Yeah, in just a little depressed I guess, I want to go home"

"Don't worry Shinji, everything will be ok"

"Well I guess…ive got mom and…you…to talk to after all"

"Your mom will always be here for you, and so will I"

"Thanks, Kyoko"

"Don't worry about it; I remember how long it took me to get you to stop calling me Ms Soryu"

"Yeah…sorry"

"You've nothing to apologize for; you're a great person Shinji. What ever girl gets you will be really lucky"

Shinji knew who he wanted it to be, and seeing that he would probably spend the rest of his days in this Eva. He decided to follow the advice Kyoko had given him during their last conversation and speak his mind.

"Umm…if I do get out of here, can I ask Asuka out on a date?"

Kyoko didn't know what to say. She was a bit shocked but at the same time flattered

"Shinji, I don't know what to say…I…"

"She's the kind of person I want to be with Kyoko"

She paused and collected her thoughts, it would be nice for Asuka to be with someone who actually, genuinely cared for her the way he did.

"It would be nice, do you actually feel like that about her"

"Yes…I do"

"Well, if we get out of this when it's all over, I'll let you take her to dinner and we'll see how it goes"

"Thank you Kyoko"

Yui chose this moment to speak

"Hay you two, is this a budding romance I see"

If Shinji could have blushed, they would have

"Mother"

She stopped him

"Don't get me wrong, I think it's sweet"

Shinji relaxed a bit, Kyoko spoke up

"Don't worry Yui they'll be fine together"

"I know, I just want to make sure my son is alright"

Shinji added

"You're ok with this mom"

"Well, I don't see anything wrong as long as you both know what you're getting into. My son is going to have a Girlfriend"

"Mother…"

Ritsuko sat at her station. The nurses had just arrived with Asuka and had helped the Technical crew load her into the Entry plug for unit 00. The plug was then inserted and activation begun. Misato, Rei, Commander Fuyutsuki and the others sat back and watched.

"Maya how does it read"

"Looking good so far"

Shinji could feel Asuka inside of the Entry plug. Her mind and soul were a jumbled mess of memories, horrible ones. One stuck out though, her mother's suicide. Shinji turned to the one person who could help him

"Kyoko, did you really do that"

"No, that was after the first activation experiment. My soul was trapped in unit 02 while my body was left living. From what Yui told me, her body didn't make it"

"So it was just your body, no soul"

"That's about it"

"Ok, I'm going to try to talk to her"

Shinji steeled himself for what he knew would be the biggest emotional shock to Asuka's system since her mom died

"Asuka…are you their"

She didn't answer but he could tell he had her attention

"I'm here if you wana talk"

"Shut up Shinji"

Her voice was weak; one could tell she hadn't spoken in a while

"It's alright Asuka; you don't have to carry this anymore"

"I don't want to talk to you baka, I hate you"

She reached down to turn the com off, only to discover it wasn't on in the first place. So how was he talking to her?

"Where the hell are you baka?"

"I'm in the Eva"

"That's bull shit; I'm the only one in the plug"

Slowly she began to wonder if they had come up with a duel cockpit version, like a trainer Eva or something

"Umm…this will be kinda hard on you but…do you remember the 14th angel Zeruel"

"What about it"

Shinji could tell the old Asuka who loved to berate and bagger him at every turn was slowly returning

"Remember what happened to me"

"Yeah you got stuck in the plug; I better not get stuck in here with you, where ever you are"

"Your…misunderstanding me…I'm in the Eva's core…the red thing in its chest…it houses the Eva's soul"

"Eva's don't have souls, their just big toys"

"No…their not…I would know"

She could tell something was seriously wrong now, Shinji was never like this. He may have been a baka pervert to her but he never talked like this. Something was wrong

"What are you saying baka"

"The Eva's have souls Asuka…human ones"

A sick feeling formed in the pit of her stomach

"Human"

"Yeah, I'm in Unit 00, probably forever. My mom is in Unit 01, and Unit 02"

She could tell where he was taking this

"Shut up baka, don't you even lie to me about that"

"I'm not lying…I guess is should just tell you…your mom is in Unit 02, from what they told me that is why we were chosen to pilot in the first place"

She slumped forward in the seat, her whole world turned upside down. Her mom wasn't gone. She then did the one thing she swore she would never do again, she cried. She cried for her mother, For Shinji's mother and surprisingly to even her, though she would never admit she did, she cried for Shinji. All three of them had been taken by the Evas. But at least there was hope now.

"Then what was hanging in that hospital room"

She shouted through her tears

"It was…just a soulless body, she want into unit 02 during the accident"

"Is she there now"

She asked betwine sobs

"Yes…I've been talking to her"

Asuka became frantic now

"Eject this damn plug baka, I have to go"

He knew what she meant; she was going to unit 02. He told Kyoko she was coming, and then ejected the Entry plug. Asuka didn't even wait for the LCL to completely drain; she just bolted from Unit 00 and headed for Unit 02.

(At Shinji's insistence Ritsuko and her Techs had prepped Unit 02 just incase she did this sort of thing.)

She climbed into the Entry plug and began insertion. After the Eva had activated she called frantically looking for her mother, Shinji may be a pervert in her mind, but he wasn't a liar

"Mama"

She waited, yearning for what came next, her mother's response

"I'm here sweetheart"

Asuka cried like a baby for the next few minuets, her tears dissolving into the LCL. There it was, well there she was. Shinji had told the truth. Asuka had never cried harder in her life both from the sadness over her mother's death, but also from joy. She wasn't gone, she was in her Eva, she could talk to her again, maybe even get her to notice her now.

"Why mama, why"

"I had to, you were to pilot Unit 02 anyway. I just wanted you safe and this was the easiest was to do it, Im so sorry sweetie"

Asuka was smiling now, in the end the only thing her mother though of was her

"Is that why you really did it mama"

"Yes sweetheart, that's why Shinji's mother went into Unit 01, to protect him. His father tricked him into Unit 00. Yui mad him pay for that"

"Is there any way to bring you back?"

She was calmer now; she had no tears left to cry

"Their trying to find a way to save Shinji as we speak, if it works for him then when this is over we can be together"

"I'm glad, thank you mama"

"Can I ask you something sweetie"

"Yes mama"

"How do you feel about Shinji?"

"I don't know, I use to think he was just a pervert and a coward but, after this, I don't know what to think. I mean, he's just so confusing"

"Would you consider going out with his once to test the waters"

"Hmph he wouldn't ask me even if he wanted to"

"He already asked my permission"

"No way, the baka already ask you if he could take me out"

"Yep"

Asuka smiled a bit

"I guess all of this gave him a spine"

"Maybe"

"Now if he would just stop apologizing all the time he be alright"

"So you do like him"

Asuka was about to say no, but didn't, she knew how she felt about Shinji, and knew her mother did to. So instead she just blushed and smiled, it was time for her to finally admit it, not just to her mother but to her self

"He can be an idiot and a coward sometimes, but still, he's not always like that. He has his moments. Mama,

"yes sweetie"

"I think I love him"

"Then tell him"

"I will, once he comes back I will"

"Good, I'm glad you could finally admit it"

"Me to"

From behind a false panel in the Cages one of the clones watched the whole event unfold. Like Rei she could hear the words exchanged in the Evas, she could also hear Asuka's soul singing for joy that her mother was still around in some way. She decided it would be best to meet up with Lilith and the others as they made their way out of central dogma.

Ritsuko had released Asuka to Misato's care after her exams reveled she was fine. On the trip home Misato and Rei under orders from Commander Fuyutsuki breaded Asuka on Rei, her origins and anything to do with the angels. To say the least Asuka was confused

"Ok, ok let me get this strait. Rei is half angel clone of Shinji's mom making them brother and sister, the Kaoru kid is the 17th angel, the 1st angel that he and the other angels were looking for in the first place was in the bastard when unit 01 smashed him, there are more Rei's, and there's an angel in bottom of the base that was responsible for the human race even existing. Oh and lets not for get the glorious fact that LCL is angel blood. Is that everything I don't already know?"

Misato nodded

"Yep you took it better than I did"

Rei decided to comment

"Yes you were nearly livid when Dr Akagi Kaoru and I briefed you"

"Don't remind me"

Asuka at back taking it all in, well when she wasn't holding on for dear life that is

Once at the apartment they left the car, the first thing Asuka did was kiss the asphalt thanking go she was alive. Upon entering the apartment they noticed the lights were off. Misato flicked the switch by the door. As the lights came on they were greeted by a shocking sight. There on the couch sat 3 girls, two of them were Rei and Asuka's age but the 3rd was almost Misato's age. The older one who had long white hair and red eyes stood

"I'm sorry about the intrusion but we must discus something of great importance"

Then her eyes fell to rei

"Hello Rei, I haven't seen you in many years. Your sisters here tell me you are doing well"

Rei's eyes widened in shock, indeed the other tow girls bore a striking resemblance to her, and she also knew whom it was addressing them

"Lilith"

The name almost caught in her throat. Misato quickly pulled her pistol and brought it into line with the angel, but then thought better of it, if the pallet rifles couldn't hurt one, what could her 9mm do. Asuka just remained quiet

"I'm glad you remember, your sisters have told me of the events that have transpired over the last few days including the accident involving your brother, ive come here to offer my assistance"

Rei found her voice again

"How so"

Lilith motioned towards the living room

"Come, sit, I shall explain all"

In a dark circular chamber the monoliths of SEELE were discussing the recent change of events. All they knew was that commander Ikari was dead and that their trusted spy Tabris had failed to report in twice. They knew they would need to move soon if the scenario was to proceed as planed. Too much time and effort had gone into this and to hell if they would just sit back while a few children and a rouge angel stopped them.

Yes they would all pay soon.

A/N Whew, im done with this one now. The story is finally falling into place and things are about to come to the final conclusion in a few chapters, so stay tuned.

Credit to D-Wrecked for the pairing.

Glory to readers and reviewers alike

Later


	5. Chapter 5 All Good Things part I

Disclaimer- don't own it, EVA or TNG

A/N Asuka will be OOC a bit from here on out due to the fact that her mom is alive somewhat. Tell me what you think. Sorry it took so long I tried to go slower to take my time.

**Shinji ZERO**

Chapter 5

All Good Things part I

End Game

Lilith's plan was simple, her normal form in Terminal Dogma was to be destroyed, then she in her human form would merge with unit 00's core and release Shinji. Then two of the other angels whose souls were trapped in the chamber of Gaff upon their destruction would enter the other two Evas and free the persons trapped with in. With Rei's assurance that Lilith could be trusted Commander Fuyutsuki ordered Asuka in Unit 02 into Lilith's chamber with two N2 devices to insure nothing of the old corpse survived. This would also end SEELE's plans for Third Impact since they needed Lilith's normal form. Also once fused into Unit 00 there was no chance her human one would be used.

Asuka sat in her Eva conversing with her mother on the slow trip into Terminal Dogma

"So have you talked to Shinji?"

"Not yet"

"You need to you know"

"I know, but now I know I'll get to see him again, so im going to wait until I can tell him in person"

"Ok"

Ritsuko monitored Asuka's descent from the main bridge control room with Misato, Commander Fuyutsuki, Kaoru, Rei's "sisters", Lilith in her human form and everyone else. Because of the danger SEELE attacking to stop this operation Rei sat in Unit 01 awaiting launch. Once Asuka hit the bottom, an area called The Valley of Death Ritsuko directed her toward liliths chamber which was sealed by what was called Heavens Doors. There crucified to a large red cross was the white angel form of Lilith Once the doors were opened Asuka wasted no time, she placed an N2 mine at the base of liliths cross and then drew her progressive knife. She cut into the angel's chest and forced a second N2 into it.

"This is Asuka, mission complete, can I come up now"

Misato responded

"Good work Asuka come on up"

Misato then paused for a moment

"Somebody wants to say hi"

Misato switched the com line over, a familiar, soft, and welcome voice filled Asuka's ears

"Hi…Asuka"

Asuka smiled contently, only one person could make her feel this way

"Hi baka, you doing ok"

Shinji was a bit taken back, Asuka had never shown him this much concern before

"Yeah I'm alright, all considering. Rei told me they found a way to get me out. That Lilith was going to take my place in here"

"Yeah, that's how it's going to work"

Lilith decided it was time to fill Nerv in on the rest of her plan

"Actually that not all"

Everyone on the bridge and Asuka in unit 02 blinked, Misato asked the obvious question

"What do you mean?"

"Well, I had not intended to bring Shinji back alone, he and Asuka have endured much in their lives. So with Tabris's help I have convinced two of the other Angels to take the places of Yui and Kyoko"

If those two could have jumped up and down with joy, they would have. Rei senesced the joy of her mother, Yui and was softly smiling in the cockpit of Unit 01. Asuka was all smiles while she conversed with an equally happy Shinji. They were finally going to find out what it meant to have a family; the three children were getting their mothers back. Then a thought occurred to Fuyutsuki

"Which angels"

Lilith just grinned

"Sachiel and Zeruel, why"

Ritsuko nodded and Kaoru commented

"Good choice the 3rd and 14th angels"

The kids didn't care; they were going to have a family by the end of the day, and Asuka. All she could think was

'I'm getting my mama back, I'm getting my baka Shinji back, my god can it get any better than this'

Asuka locked Unit 02 back into its cage after the ten minute assent from Terminal Dogma. After saying good bye to her mom she jumped out of Unit 02 and headed to the bridge.

"It's done Misato"

"Good work Asuka"

"Let me talk to baka"

Misato had never known Asuka to want to talk to shinji

"Umm…alright"

She handed Asuka the headset. She put it on and sat in the chair beside of Misato

"Hay Shinji"

After a moment he answered

"Hay…everything ok Asuka"

"Oh yeah every thing is perfect"

Shinji would have smiled if he could he had never known Asuka to be so happy.

"I've never heard you like this…you're…really happy"

"Of course my baka, in an hour my life will be prefect. I'll have my mama back, hell in an hour you and your mom will be back to"

"Yeah we will be…listen Auska…I wana ask you something later ok"

Asuka already knew what he wanted, and it made her even happier. Shinji had grown a backbone and she liked it.

"Cant wait baka, cant wait"

One of the techs announced over her Com

"We are now starting countdown sequence, close all shutters and bulkheads leading to terminal dogma and evacuate the lower sections of central dogma, Repeat close all shutters and bulkheads leading to terminal dogma and evacuate the lower sections of central dogma"

Everyone on the bridge sat in silence. Ritsuko and her staff had planed this operation to the smallest detail. The two floors above liliths chamber would be destroyed in the blast while 2 above that would take moderate damage. The floors to be destroyed included the cloning lab where Rei and her sisters were born. The MAGI records of how this was done would be deleted at the same time insuring there would never be another Rei created

"Maya initiate sequence once all personnel are evacuated from those floors"

"Yes ma'am, now on stand by for detonation sequence will commence once all personnel are evacuated"

A few moments alter the all clear came Maya reported

"Ma'am all personnel are now out of the affected areas"

"Good, start detonation sequence"

"Sequence activated T-minus 30 to detonation"

The technicians monitored the countdown on the monitors, as the count down reached the last few seconds, Maya counted the off

"Now 10 seconds to detonation

7

6

5

4

3

2

1

Detonate"

The entirety of central dogma was rocked by the force of the blast. Any technician or other personnel who were standing were thrown off of their feet. Even some who were seated were knocked over. Commander Fuyutsuki, Ritsuko, Misato and Asuka were thrown to the floor. Kaoru just steadied himself with his AT Field and Rei, who was still in Unit 01, just rode it out. After the shock had ended and everyone steadied them selves the sub commander ordered Rei in Unit 01 into Terminal Dogma to survey the damage. She reported that everything from the cloning labs and below had been totally vaporized. She then began her assent.

Ritsuko then turned to her technical team

"Now activate the erase program and destroy all data relevant to Rei from Balthazar. Then run the same program in Melchior and Casper"

"Yes ma'am"

With in a few key strokes and moments later all relevant data to Rei and any process used to create her and her sisters had been erased.

Once all relevant data was erased and Rei had returned Lilith decided it was time to commence. The commander turned to Ritsuko

"Doctor I need you to prepare a plug for Lilith, also connect units 02 and 01 directly to the chamber of gaff as Lilith instructed"

"Already on it"

A while later Unit 00's Entry plug had been prepared. Doctor Akagi and her staff had also connected Units 01 and 02 to the chamber of Gaff to commence he transfer on those two as well.

Asuka, Rei, Misato, Rei's sisters, Commander Fuyutsuki, Dr Akagi and her staff sat in the control room for the Eva cages. Rei was quietly conversing with Shinji over a com line while Asuka looked around the room. Her casual look stopped on Rei's "sisters". While her staff mad preparations for the transfer Dr Akagi had preformed exams on each of them. Rika the only one to still look slightly similar to Rei was now the only one to hold any form of DNA relation to her. The others were now individual; none of the others shared many genes. 'I guess that makes her Shinji's sister to, Im going to have to get use to this'.

Misato walked up to Rei and taped her on the shoulder. Rei removed the headset and turned to her

"Yes"

"Rei we need to go over the procedure with Shinji now ok"

She nodded

"That is fine"

After saying goodbye to him she stood and walked over to where the others were standing. Asuka knowing she needed to talk to Rei walked over to her

"Listen wonder girl we need to talk"

She pulled Rei aside and down an empty hallway

"Why did you bring me here?"

Asuka could tell she wasn't angry about being pulled like that, just curious as to why she needed to talk to her, it was time to do something Asuka never thought she would ever do

"Listen wonder girl I just …wanted to say…sorry"

Rei just tilted her head curiously and continued to listen

"I never really tried to get to know you; I was a bitch, arrogant, heartless, and im sorry. I just get frustrated and mad easily. I guess I just wanted to ask if…maybe…we could try to be friends"

Rei was impressed to say the least. With the pain mostly lifted from her Asuka was a totally different person. She smiled and nodded

"Yes I think so"

Asuka smiled back

"Thanks"

"I just have two requirements"

"What is it?"

"One, call me Rei, that is my name. And two, I ask that you not break my brothers heart"

Asuka smiled and nodded

"Sure thing, that won't be so hard"

"Well then, friend, shall we go and check on my brother"

"Yeah sure"

**A/N Whew that took a while, I hope it's good for everyone. I tried to go into more detail and will do so with the rest of the chapters. And yes I know All Good Things was the title of the last two episodes of Star Trek TNG and no I don't own that either**

**Next chapter All Good Things part II Family Ties**


	6. Chapter 6 All Good Things part II

Disclaimer- don't own it, EVA or TNG

A/N You all really like this don't you. Well there is only one chapter after this one plus the epilogue so enjoy

**Shinji ZERO**

Chapter 6

All Good Things part II

Family Ties

Everyone sat anxiously awaiting the moment of truth. Lilith had been already loaded and absorbed into Unit 00 and the connections from Units 02 and 01 to the Chamber of Gaff had been opened.

It was only a matter of time.

Each of the Eva's chest armor had been removed around the core. On unit 01 this required only removing one section of the chest armor. However on units 00 and 02 it required removing the whole chest plate. Shinji, who had been talking to Asuka at the time, likened it to someone taking off his shirt. A comment which caused the red-head Asuka to blush.

In the interim Ritsuko had chanced an examination of Rei wondering if any of this was affecting her. They could only wait for the results.

Misato and Rei with a medical team stood on the catwalk by unit 00's core. Rei with a blanket in hand to wrap around Shinji upon his return.

The Commander and a medical team stood similarly ready at unit 01

Ritsuko and Asuka stood by Unit 02 awaiting the moment Asuka's life would start anew. Shinji had assured her that he would be fine and that she should be there for her mother.

Then it happened

Misato and Rei had turned around to inform the medical team behind them of what to expect. A loud thud on the catwalk behind them alerted them; they turned to see the nude form of Shinji Ikari laying face down on the catwalk. The pair immediately rushed to his side, Rei wrapped the blanket around her brother and comforted him while Misato helped the med team load him onto a gurney for transport to the medical wing of headquarters. Misato immediately noticed one big difference in Shinji's appearance. The roots of his normally brown hair had turned the same color of blue as Rei's. The pair followed the medical team as they took him into the isolation room for examination.

A short while later Asuka walked up behind them as they waited for news. Misato who had seen her walk up and sit beside them was the first to speak

"Is it over"

Asuka nodded

"Like clockwork, baka came back, then his mom, then mama"

Rei nodded

"It's good to have her back isn't it?"

"Yeah"

Misato smiled

"How is she?"

"She woke up a little bit ago, she's resting now, and they said she'll be able to leave tomorrow once she rests"

Then Asuka decided to ask the obvious

"How's Shinji"

Misato shook her head

"No word yet"

Then a voice came from down the hall

"Ms Katsuragi"

Misato and the girls turned to look at the speaker. Standing in the center of the hall was Commander Fuyutsuki assisting a woman in a hospital gown who bore a striking resemblance to Rei, where Rei in her late 20s to early 30s with brown hair and brown eyes. Befor Misato could even speak Rei stood and walked over to the woman the Commander was assisting. She stopped a few feet in front of her, Asuka then saw the full resemblance and also something she never expected. Tears began to form in the corners of Rei's eyes as the full impact of who this woman was sank in. Her lips quivered slightly as she held back from sobbing

"Mother"

Yui smiled

"Rei"

Even the girl whose classmates had dubbed the Ice-Queen couldn't hold back her emotions anymore. She rushed forward and embraced her mother as she sobbed. Misato and Asuka smiled, Asuka because this reminded her of her own tear filled reunion with her mother and Misato because she was finally seeing the real Rei Ayanami.

For a few moments this reprieve went uninterrupted until someone at the end of the hall cleared their throat. The group turned to see Dr Akagi and the one person Rei was hoping would be here, Rika. Rei let go of her mother and walked over to the girl

"Hello Rika"

The shy and timid girl barely managed to respond

"Hello"

"Have you met out human mother?"

Rika, who looked even more like Yui than Rei did, just shook her head; Rei took Rika's hand and led her over to where Yui was standing

"Mother this is my sister Rika, Rika this is our human mother Yui Ikari"

Rika smiled at Yui who then gently and slowly, as not to scare the young girl, hugged her. Rika stiffened at the contact but soon melted into the hug. The Ikari family had just welcomed its newest members Rika and Rei Ayanami, now Rei Ikari.

Ritsuko walked over to Misato and Asuka who were just looking on smiling.

The door to the examination room opened and the doctor strode out. Ritsuko walked over to him and the two discussed Shinji's condition while the group just looked on. Finally the doctor left and Ritsuko walked up to the group

"Shinji is resting comfortably, he was awake for a few moments and the doctor reported that he was fully aware of everything that had happened. His tests all came back normal and the only anomaly reported was that hi hair…is turning light blue"

Misato spoke up

"Ritsuko does that mean he's going to…"

"No, there is no Angel DNA in his system, in fact Rei your test results came back. It seems you and your "sisters" no longer have angel DNA within you"

Rei blinked and tilted her head

"I am human"

"Yes, you are a completely normal teenage girl; you have even somehow regenerated your reproductive organs, which should begin to work soon"

Yui could only smile, not only had everything worked out, but had done so beyond her wildest dreams.

Shinji slowly opened his eyes

"Unfamiliar ceiling"

He smiled a bit; it was good to see a ceiling period never mind an unknown one. He was pulled out of his thoughts when the doors to his room opened. In walked Misato, Asuka who he wanted to talk to, Rei, another girl with blue hair he could only assume was a clone and Dr Akagi. Then the one thing he had prayed for all his life came true. Through that same set of doors, came his mother. The group stopped at his bed side. Misato, instead of her usual glomping just stood back and made room for Shinji's mother to sit at his bed side. Rei and the other girl stood on the bed side with his mother while everyone else just spread out in the room taking seats where they could. Asuka decided to be patient and let Shinji's family talk to him first. Yui stroked Shinji's hair as both mother and son chocked back tears. Finally Shinji couldn't take it any more he sat up, wrapped his arms around his mother's neck and began to cry. Yui, try as she might, couldn't speak through the tightness in her throat. After a few minuets Shinji pulled away and lay back down on the hospital bed. As she wiped the tears from his eyes Yui found her voice

"I'm so sorry Shinji; I should never have left you like that"

"Its ok mom, you did what you had to do, it hurt but your back now. Everything is fine now"

Shinji impressed everyone with his new confidence, especially Asuka 'baka has grown a pretty good back bone, and he does look good with blue hair…this is nuts I'm attracted to Shinji…but…he is attractive with that new spine of his…and he is a good guy anyway, hell why not if he asks me out I might as well go for it'

Shinji then turned his attention to his sister

"How have you been Rei?"

"I have been well, and you brother"

"Fine, I guess"

Ritsuko who stood beside of Shinji's bed on the side across from Yui finally spoke

"Shinji do you remember anything of the past few days"

He sighed

"Almost everything"

She nodded and wrote something down on her chart

"Thanks that will be all I need, as long as you get plenty of rest there is no reason for you to not go home today"

Yui looked up at her

"What about myself and Kyoko"

"Nerv has arranged for the apartment beside of Misato's to be linked to hers by knocking down the wall separating the two sitting rooms and the front door be blocked. In essence expanding the Sub-Commanders apartment to accommodate new patrons"

Misato smiled

"So Nerv will be expanding my apartment"

"Its being done as we speak, as well as having new furniture put into the rooms"

Asuka butted in

"What about me and mama"

Ritsuko turned to regard the girl

"We thought of that when we decided to do this, there will be enough room for you both when she is released tomorrow, that's if Misato will have you"

Misato just shrugged

"The more the merrier I always say, this way you and Shinji don't have to move out Asuka"

"Yes"

Life in the Katsuragi/Soryu/Ikari household was about to get interesting.

After everyone had said there hellos they all left. Misato to sign Shinji's release forms, Yui to sign the forms not only for release but to affirm that she was indeed alive. Rei had wanted to stay but opted to leave with Misato after assurances from Shinji that he would be ok, while Rika just followed her. This left Shinji and Asuka alone

"Glad your ok baka"

Shinji just lay back, smiling contently

"Yeah, well I guess everything is going to change now huh"

"Yeah"

Asuka walked over and sat on Shinji's bed side. She smiled down at the boy she had grown to like and even love

"Hay baka, can I tell you something"

"Yeah sure"

"I umm…."

She wetted her lips and looked into his brown eyes

"I-I love you Shinji"

Before the boy could say anything Asuka leaned down and pressed her lips to his. After a few moments Shinji melded into the kiss and even began to return it. He slowly snaked his arms around Asuka's waist and pulled her closer to him. After a few moments she pulled away

"Your breath doesn't tickle that bad, to tell he truth the firs time I kissed you, I held your nose so you would goof the kiss up"

"Why"

She just smiled, shook her head and blushed a bit

"I liked you even then; I just wanted to find any reason not to like you, maybe give you a reason not to like me"

"Asuka I cold never do that"

"Why not"

"Because I love you to"

In a move that shocked even Asuka, Shinji pulled the girl back down and covered her lips with his own. Asuka froze in place, totally absorbed in the kiss. Shinji's eyes fluttered open hearing the door open his glanced that way. There stood Kaoru, smiling as always. He nodded as to say 'see you later' and closed the door. Shinji closed his eyes and concentrated on this kiss.

Two days later everything was in chaos. Everyone had finally settled in at the Katsuragi/Soryu/Ikari household. Shinji and Yui were busy making dinner, Misato, Asuka, Rei, Rika and Kaoru sat at the table while Kyoko sat in the floor petting Pen Pen Misato's pet penguin while occasionally asking Kaoru questions about being an angel.

Rei and Rika had decided to share a room in the apartment's new wing while Yui and Kyoko took the other two bedrooms, all and all it was actually fun having 4 new flat mates.

Kaoru had moved into the flat next door.

Shinji just cooked on happily, sure he was now cooking for 4 more people, 2 of which were vegetarians, but the fact that one of the new people was his mother changed this from a chore to actually being fun. The fact that he and Asuka were now an item made this a dream compared to the nightmare he had initially left. His mother seeing her son deep in thought decided to speak up

"So how are you and Asuka doing?"

Shinji just smiled and blushed, Yui just nodded

"I see must be pretty well then to get you to blush like that"

"Mother"

"Im sorry Shinji, I just couldn't help it"

Shinji decided to change the subject

"I herd Commander reported the last angel destroyed"

"Well it was, your friend Kaoru is human now right"

"In a way"

His mother nodded

"So how does it feel to have naturally blue hair?"

Shinji's first act once he arrived at the newly expanded apartment was to bathe. Though the hot water was enough to remove the last traces of brown from his hair, it had steadily been changing since his return.

"Its ok I guess, when everyone sees me with Rei they will probably get the idea that were related, though Toji and Kensuke are going to grill me about it"

She nodded

"So what are they going to do about school?"

"They are going to just pick up and start next year. Now that the angel attacks are over people are coming back here"

"That's good"

Misato sat in the kitchen with Rei, Rika Asuka and Kaoru watching Asuka's mother sit in the floor and play with Pen Pen. Misato had grown accustomed to Kaoru though the knowledge that Adam was finally dead did help her accept him. Asuka looks over at Kaoru

"So what now"

"I will continue to live. I will grow old and die or I may die in my youth. But I am now free to do as I desire"

"And that is"

"I will live as a normal child and learn as I can, then I suppose once that is done I will have to, as is said, wait and see."

Suddenly the phone rings, Misato goes to get it

"Hello, Katsuragi residents"

"Hello Katsuragi"

Misato immediately takes the black cordless phone into the next room and shuts the door

"Kaji"

"The one and only, I told you I would call"

"I was starting to wonder"

"How's Shinji"

Misato faked ignorance

"What do you mean?"

"I know about what Commander Ikari did Misato, actually I know about all of it"

"How"

"That's not important now, listen day after tomorrow have the kids and everyone to Nerv by 2 pm"

"Why"

"The committee is going to make their move"

"SEELE"

"Yep, I'm going to try and pull some strings and see if I can get you and the kids some help. The JSSDF and the UN forces are prepping to move against them soon, probably while their distracted with hitting Nerv"

"So this will all end soon"

"As long as Nerv doesn't fall, yeah it will. Tell Commander Fuyutsuki everything I've told you ok, I'll see you soon Katsuragi"

Though she tried to hold them back the words slipped from her mouth, not that she didn't actually mean it mind you.

"I love you Kaji"

"I love you Misato, bye"

She hung the phone up. She walked back into the kitchen and sat back at the table. She already had begun to think about how to counter SEELE's coming attack and two day's wasn't much prep time

"Listen guys im going to Nerv don't wait up. And Shinji I expect you Rei and Asuka at Nerv by 7 in the morning for training got it"

"Why"

"I'll tell you later"

Misato grabbed her jacket, put on her shoes and headed for Nerv

**A/N That didn't take as long as I thought. The last chapter may take a bit, but only one to go plus the epilogue. **

**Thanks to my readers and reviewers.**

**Till 7 stay cool.**

**Next chapter All Good Things part III Of Love, War, and Angels**


	7. Chapter 7 All Good Things part III

**Disclaimer- don't own it, EVA**

**A/N this is it, last chapter. All that's left is the Epilogue. It's been one heck of a ride. Thanks for the reviews and to all the readers, Thnak you  
**

**Shinji ZERO**

Chapter 5

All Good Things part III

Of Love, War, and Angels

At 7am sharp the children, Kaoru, Kyoko, Yui and Rika arrived at HQ. Once they arrived Misato and Ritsuko along with Commander Fuyutsuki, who along with the staff had pulled an all nighter prepping for the SEELE attack, gathered them into the briefing room. The Commander then gave his briefing

"Ok, here is what we know. Our intelligence agents have confirmed that SEELE is indeed prepping for an assault on Tokyo 3. From those reports we can surmise that they will employ Evangelion units 5-13 in the attack"

Ritsuko stepped up

"Very little is known about these units, any information you can give will be helpful Mr. Nagisa"

Kaoru nodded

"I will tell all I know"

"Good, now in an hour Shinji, Rei, and Asuka will perform synchronization tests and training drills to prepare for the attack"

Yui spoke up

"Any chance they will employ the JSSDF in the attack"

Misato shook her head

"From what Kaji told me they are preparing to move against SEELE along with the UN"

Ritsuko sighed

"I hope so; if they do this battle could be over in a matter of minuets"

She paused befor continuing

"We've ordered a level 1 evacuation of all nonessential personnel, anyone who doesn't need to be here will evacuate to the shelters on the city outskirts with the civilians"

Kyoko looked at Ritsuko

"What about us, Me, Yui, and Rika"

"It's safer for you 3 on the bridge, anyway we could use your help"

Yui nodded

"Just tell me what you need me to do"

Kaoru nodded

"I will stay there as well; my skills would be invaluable should SEELE employ ground forces as well, and during the tests it may be helpful if I am present"

Ritsuko smiled a bit, having an Angel on the bridge during the attack couldn't hurt them at all

"Ok then, you guys know what you've do. Yui, Kyoko and Misato will go to the bridge and start configuring the MAGI to withstand outside interference such as attacks from other MAGI systems. Shinji, you Rei and Asuka will get ready for your tests which Maya Ibuki will conduct. I will be helping the tech crews sure up the defense systems inside of the Geo-Front as best we can. None of the in city defenses will be repaired as we expect to be hit with an N2 as a first volley"

The commander spoke again

"This will more than likely be done to open up the GeoFront to facilitate easier access for their Eva units"

Misato nodded

"We begin the Tests in 30 minuets Shinji, Asuka, Rei go to the lockers and get ready, everyone else, go to you designated stations and begin preparations our Intel has placed the likely attack time at 2pm tomorrow"

Shinji raised his hand

"Umm…Misato"

"Yes Shinji"

"What about the people in the shelters, will they be ok if an N2 goes off"

"Don't worry the shelters are far enough away, they'll be safe"

Kyoko slowly stood, her face showing worry

"Misato, What about Pen Pen"

Misato quickly caught on and mirrored her worry

"Oh god Pen Pen"

Misato and Kyoko bolted out the door to collect the water foul and bring him to HQ. The Commander just shook his head

"Can't live without that bird can they"

Ritsuko nodded

"Im not sure who's more mature, them, or the penguin"

Shinji, Asuka and Rei sat in the respective Evas awaiting activation. Eva 01 felt different than before. Asuka and Rei had said the same about their respective units. Maya's voice cant over the com

"Are you kids ready?"

"Yes ma'am"

"Leave it to us"

"I'm ready"

"Ok then, now beginning entry"

Shinji felt his entry plug descend into the Eva. After a few moments the screens came on

"All Eva activated"

"No problems detected"

The next voice Shinji herd over the com line was Kaoru's

"Shinji, Zeruel should be able to here you now, remember speak with your thoughts not your words"

"Umm…ok"

Shinji sat back and concentrated on Unit 01

_Are you there?_

He got his response a moment later

_So you are the warrior who defeated me in combat_

_I'm sorry about that_

_Do not be, you should be proud of your skills, they are most impressive. I look forward to joining with you in battle against our common foe_

Shinji smiled, mabe this wasn't going to be so bad after all

Asuka sat in her plug, trying her best to talk to the Angel's soul in her Eva

"_Hey anybody home"_

The reaction wasn't what she expected

"_Hi there, who are you"_

It sounded like a little boy

"_Im Asuka Langley Soryu, who are you"_

"_I'm Sachiel, have you seen any of my brothers or sisters"_

"_Huh"_

"_You know Tabris or Zeruel"_

"_Oh I get what you mean, Kaoru right"_

"_I think that's the name he goes by"_

"_He's in the control room right now, I'll tell him you said hi ok"_

"_Thanks, will we be fighting today"_

"_No, tomorrow"_

"_Ok, I'm going to sleep ok, I'll see you tomorrow, bye"_

Asuka could only smile; she hadn't expected the angel to be this, well, perky

"_Ok bye"_

In unit 00 Rei was having a much easier time in talking to Lilith since she already know what to expect

"_It seems the others have bonded well Rei"_

"_Yes it would seem so"_

"_I'm glad you have finally become the person you wanted to be"_

"_Yes, I have a family, I am finally happy"_

"_Good, so how does it feel to be human now?"_

"_Much better"_

"_Good, listen I know that you no longer carry a part of me with in you, however, I was wondering, if you would still call me mother"_

"_Of course I will, as will Rika. Yui Ikari is our human mother, you are our Angel mother"_

"_Thank you for that, my daughter"_

After a hard day the children were finally able to rest. They were all give quarters inside of Nerv for safety reasons. Agents from section two had packed everyone's belongings and brought them to HQ, even Kaoru. Asuka and Shinji decided to go for a walk about inside the GeoFront to help take their minds off of tomorrows coming battle.

"So baka nervous"

"Yeah a bit, but, Zeruel is a fighter by nature, I'll be fine"

"Good"

As they walked Asuka slowly slid her hand into Shinji's. The pair walked on towards the lake, hand in hand. Shinji finally turned to Asuka

"How's Unit 02"

"You mean Sachiel"

"Yes"

"He's ok, more like a 4 year old than an angel, but ok"

"Good"

"Hay Shinji"

"Yeah Asuka"

"Can I sleep in your room tonight?"

He was a bit taken back to say the least

"What…"

"Don't get any perverted thoughts third, one of us might not come back tomorrow, I just want to be near you"

"I'm not going to die Asuka, and I know you won't either, but if you want to you can"

"Thanks baka, you better not tell a soul about this though"

"I won't"

"Good boy"

Else ware in Nerv Misato, Yui, Ritsuko, and Kyoko sat on the bridge going over the last of the preparations. They traded stories of collage life and Misato brought Yui up to date on her son

"So he's really that timid huh"

Misato nodded

"Yeah, but ever since he came back I've been noticing little things bout him"

"Like what"

"Well he's more confident now, he's harder to tease"

Yui shook her head

"That's a matter of opinion, you just gota push the right button"

"Well anyway, he's developed a lot, especially where Asuka is concerned. But I think part of that is her opening up to him. Not just his opening up, which he has"

Yui smiled

"Thank you for taking care of him for me"

"Don't worry about it; I doubt I'll ever have any, so these kids are as close as I'll ever get to having my own"

"Still, Gendo abandoned him; I should never have tested Unit 01. I shouldn't have left him alone like that. If I had know, I wouldn't have"

Kyoko just shook her head

"He doesn't blame you, he told you that remember"

"Yeah I know, so on a lighter note, how does it feel for your daughter to be dating my son"

"It's not so bad; Asuka could use a gentleman like Shinji in her life. Who knows maybe they'll get married and have kids some day"

Ritsuko added

"That may be more possible than you know"

Misato tilter her head a bit

"What do you mean Ritz?"

"well, a while back I had the MAGI chew some numbers and according to my results the drop in the birthrate will actually stop soon and level out at around even one death per birth, so we will have an even world population of about 2 billion"

Yui smiled and nodded

"That's good to hear, I wonder if Rei and Rika will ever have kids"

Misato shook her head

"We'll worry about that later, right now girls its time for an all nighter"

They groaned and went back to work

Rei and Rika had just settled into their room Nerv had provided for them. Rika was nervous about the next day

"Do you think we'll make it sister?"

Rei smiled and walked over to where her sister was preparing her bed. She gently wrapped her arms around her from behind

"Of course I do, we will have everyone looking out for us. Kaoru will be on the bridge, stay near him and the others and you will be fine"

He sister turned to face her

"I worry about you sister, you will be on the field of battle not I"

Rika put her arms around Rei. Rei felt it ironic that she was the one giving emotional support while only a short time ago she had no clue of them.

"Don't worry, mother Lilith will be with me. Shinji and Asuka will also be with me, I am not afraid"

Shinji had just settled down to bed. He knew he would have to let Asuka in soon so he decided to wait by the door. After a few minuets a gentle taping alerted him. He got up and went to the door, there he found Asuka in her PJs carrying a pillow. He let her in without hesitation and closed the door. Befor he could take another step he found himself pushed back against it with Asuka's lips pressed to his own.

After a moment she pulled away

"I've been waiting to do that all day"

"I'm glad you did"

The pair walked over to the bed, Shinji pulled back the covers and allowed Asuka to lay down first befor climbing in him self. He then pulled up the covers up over them and rolled over to face Asuka. She laid her head on his shoulder and snuggled up to him.

"Goodnight Shinji"

He gently kissed her on the forehead.

"Goodnight Asuka"

He hesitated for just a moment

"I love you Asuka"

She smiled and snuggled closer

"I love you to, my baka Shinji"

Asuka nodded of to sleep after a few moments. Shinji just looked at his girlfriend; he had never seen a girl so beautiful. He never thought this would happen, here he was holding Asuka Langley Soryu of all girls, watching her sleep. But their hardest trial would come tomorrow, SEELE's attack.

Yui decided to check on her son befor bed. As she approached his door she saw Kyoko standing out side of it

"What's up Kyoko?"

"Shh"

Yui walked over to her and looked in the door. There lay Asuka cuddled up next to Shinji as they slept. As a mother this made her feel two things. Joy that Shinji had found some one he loved, and dread ant what the pair could have already done

"Kyoko they didn't, did they"

"No I followed Asuka here, I was going to say goodnight and saw her going down the hall. What do you say we leave these two love birds alone for the night, and if nothing happens, maybe we'll let this become normal?"

"I don't know Kyoko"

"Come on Yui have you ever seen his that happy, I know Asuka hasn't been"

Yui had to relent that fact

"Well see"

At 11am sharp Nerv began its preparations. The children changed into their plug suits and awaited the order to go. On the main bridge everyone sat ready, all necessary preparations had been made the previous night. Kaoru had informed then that SEELE would probably employ the MP Type Eva unit in this attack and that they were probably operating under the assumption that Lilith was still where she was suppose to be. And thus they waited.

At 12 noon the city was evacuated as were all nonessential Nerv personnel

At 1 o clock the Eva's were readied for launch

At 1:30 the pilots boarded their entry plugs and began what they would later describe as the longest 30 min of their lives.

Then at 2PM the entire complex was rocked by a massive explosion. An N2 bomb had been droped. The resulting blast ripped the top from the GeoFront and destroyed what was left of Tokyo 3. After the heat had dissipated the Eva's got the order to launch.

Upon reaching the surface the three Eva's saw a sight that would strike fear into anyone.

Nine vultures like Eva's circling overhead, Shinji contacted Kaoru on the bridge.

"Kaoru, how much do you know of these things"

He shook his head

"All I know is that if you do not destroy the core they will regenerate"

Asuka chimed in

"Just like an angel right"

Kaoru nodded

"More a less"

Shinji readied himself as each of the three Nerv Eva's pick up a progressive sword.

"Ok here we go"

Shinji then began to concentrate on Unit 01 as the locking clamps released

"_Zeruel are you there"_

"_I am young warrior"_

"_Its time, we have to pierce their cores or they'll regenerate"_

"_I know, then let us do so"_

"_Yeah, let's do this"_

Each of the MP Types landed in turn, surrounding the three Nerv Eva's. Asuka got a good look at them as they all retracted their wings

"God their ugly, Misato do they have pilots"

"Just a second, nope, dummy plugs take them out"

"As good as done"

The MP Types broke into groups of three. Each group going after a Nerv Eva, Shinji contacted the girls over the com.

"Girls be careful"

"Why wouldn't we be baka, im not gona die on you"

"I will be fine brother"

They readied themselves as the MP Types stood motionless. Then they attacked.

Shinji managed to hold off the three MP Types for a few moments, following Zeruel's advice to look for an opening, which he saw as one of them missed a swing. He grabbed hold of it and shoved his sword through its chest, fracturing its core, silencing it. As the next one tried to decapitate him he shoved its now dead partner in the way. The MP Eva's sword jammed into the dead one giving Shinji another chance; he quickly pulled his sword from the first one and impaled the second, the Progressive sword breaking off at the hilt after silencing the second one. He then picked up its weapon only to have it instantly transform into the Lance of Longinus. Rei sees this and immediately advises her teammates to drop their swords and grab a lance, which they do.

Unit 01s remaining MP Eva opponent attacks, foolishly it tried to slice unit 01 in two. The Eva merely drops to one knee and ducks the attack. Unit 01 then thrusts its lance into its last opponent, silencing it. Shinji hears a familiar voice call over the radio

"Shinji, help"

"Asuka"

He turns unit 01 toward Unit 02 and sees the last Eva she was fighting about to impale her with its lance. Shinji directed Unit 01 to save Asuka, he drew back to throw his lance hoping to hit the MP Type and save Asuka. As the MP Type was about to thrust down a volley of missiles struck its head disorientating it, on the bridge everyone was in awe, there coming over the lip of the now exposed GeoFront were JSSDF VTOL's and UN fighter aircraft. Misato was ecstatic

"The JSSDF and the UN came through, thank you Kaji"

The VTOL's surrounded the MP Evas and unloaded their ordinance into them while the fighters went for the SEELE drop craft. Asuka took the indicative and picked up her lance, however befor she could throw another lance struck the MP dead in the chest silencing it. The same Lance unit 01 had held

"Thanks baka"

"Anything for my Asuka"

As the two Evas surveyed the area Rei finished her last opponent, she turned Unit 00 toward the others

"It seems this is finished"

Her brother nodded

"We'll stay out here for a bit though"

Asuka agreed

Back on the bridge the Techs were celebrating along with Kaoru, Yui, Kyoko, Misato, Ritsuko and Rika. One of the techs monitored an incoming transmission; it was from the secretary general of the UN. The bridge became quiet as the line was patched through

"Commander Fuyutsuki"

"General"

"I must say Nerv has impressed me, beating such long odds like this. I have good news"

"Yes general"

"The 12 members of SEELE have been either rounded up or killed"

Everyone broke out into cheers, even the pilots. Commander Fuyutsuki quieted them

"Anything else general"

"Yes, unfortunately Committee chairman Keel managed to transmit the plans for their Evas on an open channel, anyone on earth who may have been listening could have received them. Hell the fax machines in UN HQ here in New York have been printing them out"

Everyone turned somber; this meant that any two bit dictator with enough money and recourses could get their hands on an Eva

"That is…distressing to say the least"

"Exactly, which is why as of 0400 hours tomorrow Nerv will be officially reorganized, its mission not longer to stop the angels, but to protect against misuse of Eva technology by parties around the world"

Everyone in Nerv was shocked, but the world still need them.

Shinji, Asuka and Rei stayed on with Nerv, as did their mothers and Kaoru.

Tokyo 3 was rebuilt around the now exposed GeoFront.

Kaji retired from the JSSDF and rejoined Nerv as the head of Section 2, he and Misato married some months later though the impromptu families still live in the same flat.

Hikari, Toji Kensuke and all of Tokyo 3's former residence returned to the former fortress city and life returned to normal, well as normal as things get in Tokyo 3.

**A/N Whew that was tiring. Well now I only have the Epilogue left.**

**Thanks to all of my readers and those who reviewed, this has been a blast. Good night and Good luck  
**


	8. Epilogue A Time To Shine

Disclaimer- don't own it

A/N Thanks to all of my Readers and Reviewers. You guys and gal's rock.

**Shinji ZERO**

Epilogue

A Time to Shine

Much has happened over the intervening year since the defeat of SEELE.

Nerv and the Eva's have held off 4 world power grabs by ruthless dictators with Evangelions

The city of Tokyo 3 has been rebuilt around now exposed GeoFront

Misato and Kaji have married, though the entire group (Misato, Kaji, Yui, Kyoko, Rei, Rika Shinji, and Asuka) continue to live in the same flat. Against what one would expect everyone gets along rather well in the close proximity. Kaji decided to take the surname Katsuragi as a way of finally laying his past to rest.

In the intervening year Ritsuko, her staff, Yui, and Kyoko developed the Eva Bio Control Computer, a device that replaces the need for an Eva to have a core with an actual control system.

The entry plugs had also been modified. Now that the pilots no longer needed to sync with the Eva as much as before a standard butterfly stick and petal control setup was placed into the plugs, though they still needed a new synthetic LCL. (Think Gundam cockpit controls in an Entry Plug)

After the development of this system Lilith, still as a human, left Unit 00. After the new Bio Control Computer had been installed in Eva's 02 and 01, Lilith resurrected Sachiel and Zeruel as humans. Sachiel as a 4 year old boy and Zeruel a 15 year old, she and the others took the surname Nagisa and moved in with Kaoru, Lilith legally becoming his mother.

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That night was a good one, Toji, Kensuke and Hikari had come back to Tokyo 3 for good. The three were on their way over to the Katsuragi/Ikari/Soryu

Residence for a Misato planed party to celebrate the resurrection of the city and their homecoming. Hikari arrived first. The first thing she noticed was that the apartment was now twice its original size. The second thing she saw was her friend Asuka, lying on the couch, to her surprise with someone else, with blue hair. Just for a moment she cringed, the way they were holding each other screamed boy friend girlfriend. But only one person she knew had blue hair 'oh god please don't let that be Rei' she thought. But she was surprised when the blue haired person sat up a bit, it was Shinji. Upon him telling her of her friend arrival Asuka jumped up and walked over to her

"Hi hikari come in"

"Hay Asuka, it's been a while hasn't"

She looked around, still marveling at the flats new size

"What happened to the place?"

"Well, Baka's mom and sisters moved in so we needed more space. Nerv bought the two flats and knocked the wall down"

"That's cool"

"I got more good news though"

"What is it?"

"Two things, first I wanted you to be the first in our class to know since you're the class rep. Shinji and I have been dating for quiet a while"

Hikari smiled

"That's great Asuka, what's the second thing"

"Its incredible hikari, ya know how sometimes you dream about getting someone back you lost"

The girl nodded

"It happened to me; remember how we told you my mama died"

Hikari nodded again, Asuka pointed to the kitchen table; she then turned back to Hikari and put her hands on her shoulders. Tears visible in her eyes, but she was smiling

"Hikari, my mama is sitting at the table my dream came true"

To say hikari was happy for the pair was an understatement, they had not only found each other, but had gotten their mothers back as well, and then Hikari remembered something Asuka had said

"Wait, what did you mean, Shinji's sisters"

"Yeah umm, we found out right befor the last angel that Rei was Shinji's sister"

"Are you kidding, Rei Ayanami"

Asuka shook her head

"Rei Ikari now, surprisingly, finding out she had a brother thawed our 'Ice Queen' out a lot, we've actually become friends"

Hikari could only smile again

"That's great Asuka"

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Toji and Kensuke arrived a bit later; the first thing they noticed about Shinji was his now blue hair. They sat in the living room grilling him about the last year.

"Guys I cant tell you much"

Kensuke just shook his head

"All we want to know is, why you dyed your hair to match Rei's and are you really dating the Red Devil"

Shinji sighed, he knew this was coming

"Ok one, my hair was always this color, the gene was just recessive until last year and in case you're wondering Rei is my sister"

Toji and Kensuke's jaws were on the floor, the girl they had known since 7th grade was in fact their best friend's sister. Shinji knew the part about the recessive gene was a lie, but he coudn't say anything else.

"And two, yes I'm dating Asuka, and I'm doing so quite happily thank you"

Toji fainted, after he recovered he and Kensuke looked at Shinji in shock, Toji thought about the way Shinji had admitted his relationship with Asuka, then realized something

"Dude, were you just, acting like a smart ass"

"Yeah a bit, sorry"

"Oh hell no don't be"

Then a female voice called from the kitchen door

"Watch your language boys there are ladies in this house"

There stood the woman the two considered a goddess, Misato Katsuragi, and then a glint on her hand caught Kensuke's eye. He readjusted his glasses and screamed like a girl when the golden object on her finger came into focus

"Is that a wedding ring?"

Misato nodded

"Yep, Kaji and I marred a while ago, I thought Shinji told you"

The blue haired boy in question just shook his head

"Haven't had a chance"

Then a blue haired girl who looked a lot like Rei walked into the living room and sat beside of Asuka and Hikari who had gone unnoticed by all in the room but Shinji. Toji was the first to ask the obvious

"Dude who's that"

Kensuke nodded

"Yeah Shinji"

He turned to the girl now on the sofa

"Hay Rika"

"Yes Shinji"

"Could you come here a second"

"Sure"

Shinji marveled at how quickly Rita had progressed as a person, still Rei's progress made hers pale in comparison. Rika waked over to where Shinji was sitting and sat beside of him

"What do you need?"

"Rika these are my friends Toji and Kensuke, guys this is Rika Ikari, my other sister"

Now they were really confused

"But what about Rei"

"She's in the kitchen with mom, oh and you can come out now Asuka"

Said girl stood up, Toji and Kensuke nearly ran when she walked over to where they were

"Hay Rika, mind if I sit with Shinji, you can have the TV"

"Ok"

The blue haired girl got up and went back to the TV, Asuka meanwhile, to the other two stooges horror, sat on Shinji's lap and put her arms around his neck and kissed him

"OH THE HORROR"

They screamed

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The first day back at school had been normal. Well as normal as could be expected. Shinji received dirty looks from nearly every guy in class except the two other stooges. Asuka, to prove her relationship with Shinji, and maybe break some hearts, kissed the boy right in front of the class. Then three new students were introduced.

"Hello my name is Kaoru Nagisa; it is nice to meet you all"

"Im Zeruel Nagisa, Kaoru is my brother, it is a pleasure"

All the girls except Rei and Asuka and Hikari had stars and hearts in their eyes, the two boys, who looked almost identical except for a few details, were hot.

Then came the third, a girl who looked almost exactly like Rei strode into the door. Now word in this school, like all to others, travels fast. And the fact that Shinji and Rei were brother and sister had been confirmed by them at the start of class. The fact that the teacher called out Rei Ikari, instead of Ayanami during roll and that they now had the same hair color also helped, now this

"Hi ya, i'm Rika Ikari, nice to meet ya"

'Oh yeah' Shinji thought 'life has gotten good'

And it had, piloting Eva wasn't painful anymore. He had the girl of his dreams. He had his sisters and his friends at his side. And most of all, he had Misato and his Mother.

The lives of the Eva pilots had finally begun to settle down, though they sometimes had to do regular Nerv stuff and fight, it was a dream compared to the hell their lives had been.

It was finally time to rest.

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That night Shinji and Asuka walked through the park, things had quieted down as the city slipped into bed. They stopped under a tree and looked up at the now visible stars. Asuka just sighed and placed her head on Shinji's shoulder. Shinji had finally worked up the courage to as Asuka the most important question of his life.

"Hay Asuka"

"Yeah"

"We've been together for a while"

"I know"

"I wana ask you something, don't flip though ok"

"I won't"

What Shinji did next shocked the crap out of her. He slipped from the bench, fell to one knee and pulled a gray box from his pocked, she instantly caught on, he was proposing

"I've never been this happy before, and I don't ever want it to end. Sure we've had our rough spots in the past, but we got through it. I know were still young but. Asuka will you marry me"

He opened the box, inside was a 10 k diamond set on top of a simple gold ring, Asuka couldn't believe it, he actually did it. She couldn't hold back anymore. She wrapped her arms around the boy and began to cry

"Yes Shinji, yes I'll marry you"

Shinji pulled back a bit and slid the ring onto her finger. She immediately wrapped her arms back around him

"I love you Shinji Ikari"

"I love you to Asuka Langley…Ikari"

Oh yes they could now finally be happy.

**A/N Thank you all for joining me on this adventure. And yes all, I left the ending open so their may be a sequel some day. **

**But as for this, the ride is over.**

**The final die is caste.**

**Thank you all for your support**

"**Good Night and Good Luck"**


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